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ABSTRACT The physical organization of DNA within the nucleus is fundamental to a wide range of biological processes. The experimental investigation of the structure of genomic DNA remains challenging due to its large size and hierarchical arrangement. These challenges present considerable opportunities for combined experimental and modeling approaches. Physics‐based computational models, in particular, have emerged as essential tools for probing chromatin structure and dynamics across a wide range of length scales. Such models must necessarily be capable of bridging scales, and each scale presents its own subtleties and intricacies. This review discusses recent methodological advances in genomic structural modeling, emphasizing the need for multiscale integration to capture the hierarchical organization and molecular mechanisms that underlie chromatin structure and function. We present an analysis of state‐of‐the‐art methods, as well as a perspective on challenges and future opportunities across length scales ranging from bare DNA to nucleosomes and chromatin fibers, up to TAD and chromosome‐scale models. We emphasize models that connect genome organization to gene expression, models that leverage emerging machine learning capabilities, and models that develop multiscale approaches. We examine gaps in experimental data that computational models are poised to address and propose directions for future research that bridge theory and experiment in DNA structural biology.
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The Fracture of Highly Deformable Soft Materials: A Tale of Two Length Scales
The fracture of highly deformable soft materials is of great practical importance in a wide range of technological applications, emerging in fields such as soft robotics, stretchable electronics, and tissue engineering. From a basic physics perspective, the failure of these materials poses fundamental challenges due to the strongly nonlinear and dissipative deformation involved. In this review, we discuss the physics of cracks in soft materials and highlight two length scales that characterize the strongly nonlinear elastic and dissipation zones near crack tips in such materials. We discuss physical processes, theoretical concepts, and mathematical results that elucidate the nature of the two length scales and show that the two length scales can classify a wide range of materials. The emerging multiscale physical picture outlines the theoretical ingredients required for the development of predictive theories of the fracture of soft materials. We conclude by listing open challenges and directions for future investigations.
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- Award ID(s):
- 1752449
- PAR ID:
- 10229711
- Date Published:
- Journal Name:
- Annual Review of Condensed Matter Physics
- Volume:
- 12
- Issue:
- 1
- ISSN:
- 1947-5454
- Page Range / eLocation ID:
- 71 to 94
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1146/annurev-conmatphys-042020-023937
